Contacts of the helix formed by residues 94 - 117 (chain B) in PDB entry 5HNK
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 94 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92B GLN 3.8 2.0 + - - +
93B ARG* 1.3 77.6 - - - +
95B GLU* 1.3 74.6 + - - +
96B GLU* 3.8 7.0 + - - +
97B GLU* 3.1 37.3 + - - +
98B LYS* 3.1 23.3 + - - +
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Residues in contact with GLU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B THR* 1.3 82.6 - - - +
96B GLU* 1.3 62.6 + - - +
98B LYS* 3.5 10.1 + - - +
99B ALA* 3.2 23.6 + - - +
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Residues in contact with GLU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B THR* 3.3 7.7 + - - +
95B GLU* 1.3 77.3 + - - +
97B GLU* 1.3 60.3 + - + +
99B ALA* 3.5 7.0 + - + +
100B LEU* 3.1 47.7 + - + +
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Residues in contact with GLU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B GLN 5.0 0.3 - - - +
93B ARG* 3.5 21.2 - - + +
94B THR* 3.1 39.6 + - - +
96B GLU* 1.3 75.8 - - + +
98B LYS* 1.3 59.3 + - - +
100B LEU* 3.8 8.2 - - + +
101B ASP* 2.8 40.9 + - - +
10X C 5.5 2.4 + - - -
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Residues in contact with LYS 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B TYR 5.1 2.2 - - - +
91B ALA 5.5 3.1 - - - +
93B ARG* 3.6 49.8 - - + +
94B THR 3.1 22.0 + - - +
95B GLU* 3.7 9.0 - - - +
96B GLU 3.4 0.2 - - - -
97B GLU* 1.3 74.9 - - - +
99B ALA* 1.3 56.5 + - - +
101B ASP* 3.5 1.4 + - - +
102B GLU* 3.0 55.1 + - - +
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Residues in contact with ALA 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B GLU 3.2 14.0 + - - +
96B GLU* 3.7 6.7 - - - +
98B LYS* 1.3 76.3 - - - +
100B LEU* 1.3 66.0 + - + +
102B GLU* 3.6 9.4 + - - +
103B GLN* 3.3 21.7 + - - +
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Residues in contact with LEU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LYS* 5.5 4.9 - - - -
36B HIS 5.1 2.7 - - - +
37B ASN* 3.7 44.6 - - + +
39B SER 5.7 2.2 - - - +
96B GLU* 3.1 39.1 + - + +
97B GLU* 3.8 8.1 - - + +
99B ALA* 1.3 74.4 - - + +
101B ASP* 1.3 62.8 - - - +
103B GLN* 3.4 14.9 + - - +
104B PHE* 2.9 29.8 + - - +
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Residues in contact with ASP 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LYS* 3.0 32.4 + - - -
90B TYR* 4.1 9.0 - - - -
93B ARG* 3.1 43.1 + - - +
97B GLU* 2.8 25.3 + - - +
98B LYS 3.8 0.2 - - - +
100B LEU* 1.3 74.7 - - - +
102B GLU* 1.3 53.2 + - - +
104B PHE* 3.1 5.1 + - - -
105B PHE* 2.8 55.3 + - + -
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Residues in contact with GLU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ARG* 5.3 5.0 + - - +
98B LYS* 3.0 46.5 + - - +
99B ALA* 4.0 8.6 - - - +
100B LEU 3.4 0.2 - - - -
101B ASP* 1.3 76.9 - - + +
103B GLN* 1.3 60.6 + - - +
105B PHE* 4.5 3.9 - - - +
106B GLU* 3.2 26.3 + - - +
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Residues in contact with GLN 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B SER 4.4 8.8 - - - +
40B LYS* 3.9 39.6 - - - +
99B ALA 3.3 11.4 + - - +
100B LEU* 3.6 16.6 - - - +
101B ASP 3.3 0.4 - - - -
102B GLU* 1.3 74.8 - - - +
104B PHE* 1.3 65.4 + - - +
106B GLU* 3.3 8.6 + - - +
107B TYR* 2.9 61.0 + - + -
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Residues in contact with PHE 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B GLY 3.4 34.8 - - - -
32B PHE* 3.6 33.7 - + - -
34B PHE 4.7 0.2 - - - -
35B LYS* 3.7 40.2 - - + -
43B PHE* 3.7 22.4 - + - -
100B LEU 2.9 18.5 + - - +
101B ASP* 3.1 4.7 + - - +
103B GLN* 1.3 76.1 - - - +
105B PHE* 1.3 84.1 + + - +
107B TYR* 3.3 9.6 + - - +
108B LEU* 2.8 38.5 + - + +
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Residues in contact with PHE 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B THR* 5.7 0.9 - - + -
32B PHE* 4.1 20.9 - + - -
35B LYS* 5.5 1.6 - - - -
90B TYR* 3.5 28.5 - + - -
101B ASP* 2.8 44.6 + - + +
102B GLU* 4.5 4.0 - - - +
104B PHE* 1.3 91.0 - + - +
106B GLU* 1.3 64.3 + - - +
108B LEU* 3.8 17.1 - - + +
109B LYS* 3.1 23.6 + - - +
3Y A 6.2 2.9 - - + -
4Y A 3.6 51.6 - + + -
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Residues in contact with GLU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B GLU 3.2 21.1 + - - +
103B GLN* 3.5 7.0 - - - +
105B PHE* 1.3 76.7 - - - +
107B TYR* 1.3 74.2 + - + +
109B LYS* 3.4 9.8 + - + +
110B ASP* 3.2 32.9 + - - +
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Residues in contact with TYR 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B LYS* 3.4 30.1 + - - -
41B LYS 3.8 11.0 - - - -
42B PRO* 3.8 38.2 - - + +
43B PHE* 3.5 30.2 - + + +
44B ALA* 4.6 3.3 - - - +
103B GLN* 2.9 45.8 + - + +
104B PHE* 3.5 4.9 - - - +
106B GLU* 1.3 87.6 - - + +
108B LEU* 1.3 59.2 + - - +
110B ASP* 3.3 14.6 + - - +
111B ALA* 2.9 27.7 + - - +
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B GLY 4.4 4.9 - - - +
28B THR* 4.3 30.7 - - + +
31B GLY* 3.6 25.6 - - - -
32B PHE* 5.3 0.4 - - + -
43B PHE* 3.8 13.9 - - + -
47B TYR* 4.2 15.5 - - + -
104B PHE* 2.8 41.1 + - + +
105B PHE* 3.8 19.3 - - + +
106B GLU 3.3 0.4 - - - -
107B TYR* 1.3 69.4 - - - +
109B LYS* 1.3 60.0 + - - +
111B ALA* 3.3 3.4 + - + +
112B PHE* 2.9 34.5 + - + +
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Residues in contact with LYS 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B PHE 3.1 14.1 + - - +
106B GLU* 3.6 12.3 - - + +
108B LEU* 1.3 77.2 - - - +
110B ASP* 1.3 64.3 + - - +
112B PHE* 3.3 7.3 + - - +
113B GLU* 3.0 30.0 + - + +
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Residues in contact with ASP 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ALA* 3.9 11.7 - - + +
106B GLU* 3.2 25.4 + - - +
107B TYR* 3.7 18.0 - - + +
108B LEU 3.3 0.2 - - - -
109B LYS* 1.3 82.7 + - - +
111B ALA* 1.3 61.0 + - - +
113B GLU* 3.4 18.8 + - - +
114B LEU* 3.0 30.5 + - - +
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B PHE* 4.1 8.7 - - + -
44B ALA* 3.6 23.3 - - - +
47B TYR* 3.7 36.0 - - + -
48B VAL* 4.0 1.0 - - - +
107B TYR 2.9 14.4 + - - +
108B LEU* 3.3 10.7 + - + +
110B ASP* 1.3 74.5 - - - +
112B PHE* 1.3 58.3 + - - +
114B LEU* 3.4 2.9 + - - +
115B CYS* 3.0 28.4 + - - +
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Residues in contact with PHE 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B GLY* 4.5 5.2 - - - -
28B THR* 5.0 2.5 - - - -
47B TYR* 4.2 17.0 - + - -
65B VAL* 4.1 10.3 - - + -
66B LEU 3.9 8.7 - - - -
67B GLY* 3.3 35.9 - - - -
108B LEU* 2.9 21.4 + - + +
109B LYS* 3.7 7.4 - - - +
110B ASP 3.3 0.4 - - - -
111B ALA* 1.3 74.7 - - - +
113B GLU* 1.3 63.6 + - - +
115B CYS* 3.4 7.5 + - + +
116B LYS* 3.2 33.9 + - - +
121B THR* 3.4 29.3 - - + +
122B PHE 4.2 0.4 - - - -
123B THR* 3.5 24.5 - - + -
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Residues in contact with GLU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B LYS* 3.0 17.1 + - + +
110B ASP* 3.6 24.5 - - - +
112B PHE* 1.3 76.5 - - - +
114B LEU* 1.3 66.1 + - + +
116B LYS* 3.2 27.3 + - + +
117B THR* 3.7 8.6 + - + +
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Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ALA* 3.9 33.0 - - + +
45B SER* 3.9 13.7 - - - +
48B VAL* 4.0 11.8 - - + +
110B ASP 3.0 16.3 + - - +
111B ALA 3.7 4.5 - - - +
113B GLU* 1.3 78.3 - - + +
115B CYS* 1.3 62.7 + - - +
117B THR* 2.5 41.0 + - + +
118B THR* 4.0 2.6 + - - -
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Residues in contact with CYS 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B TYR* 4.3 5.4 - - + -
48B VAL* 3.6 16.1 - - + +
51B ILE* 4.1 10.3 - - - -
65B VAL* 3.7 34.3 - - - -
111B ALA 3.0 17.1 + - - +
112B PHE* 3.4 11.2 - - + +
113B GLU 3.3 0.2 - - - -
114B LEU* 1.3 77.8 - - - +
116B LYS* 1.3 55.5 + - - +
118B THR* 3.0 19.1 + - - -
119B PHE* 3.0 25.3 + - - +
121B THR* 3.5 15.9 - - + +
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Residues in contact with LYS 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B PHE* 3.2 35.7 + - - +
113B GLU* 3.2 17.3 + - - +
115B CYS* 1.3 74.8 - - - +
117B THR* 1.3 60.6 + - - +
118B THR 3.4 0.5 + - - -
119B PHE 3.8 7.9 + - - +
121B THR* 3.6 35.0 + - + +
123B THR* 5.2 10.6 + - - +
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Residues in contact with THR 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B GLU* 4.1 9.9 - - + +
114B LEU* 2.5 36.7 + - + +
115B CYS 3.2 0.2 - - - -
116B LYS* 1.3 78.9 - - - +
118B THR* 1.3 66.6 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il